Dear Rajesh,
In addition to the R/Rfree, you also need to look at issues like
stereochemistry, bad contacts, clashes, the general fit into density,
unmodelled ligands/waters, Ramachandran outliers, correct side chain
rotamers etc etc. I would advice you to spend (a lot of) time visually
inspecting your model and the density, and also make use of servers like
MolProbity or WhatIF to examine the quality of your model.
Fred is very right that the idea of refinement is to produce a model
that agrees with all the data, and not just one with lower R values.
cheers
Ganesh
Le 24/01/13 11:12, rajesh harijan a écrit :
Dear All,
I am working on a perfectly twinned data in space group P31.
when I refine this data with phenix refine the R/Rfree is 26.6/29.4
and average B-factor is 38.
I did one test now.....
I used phenix refined pdb and refine with refmac5 and got R/Rfree of
26.2/29.7 and average B-factor is 64.
Now I used refmac5 refined pdb and refined with phenix again. Now
R/Rfree is 22.1/24.8 and average B-factor is 56.
My question is, why B-factor gone up now and R/Rfree reduced. In which
refined model should I believe in. If last refined model is true then
how should I reduce the B-factor?
Thank you
Rajesh
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With regards
Rajesh K. Harijan
Phd Researcher
Department of Biochemistry,
University of Oulu,
Oulu, Finland- 90014
Off Phone: +358 85531174
Mob: +358 400408258
